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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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) 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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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) 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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ), 'gf_id' => 'HOM05D001186', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001186' ), 'data_identifier' => 'HOM05D001186', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001186', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35790' => 'bna', 'A01p35980' => 'bna', 'A02p15000' => 'bna', 'A03p40770' => 'bna', 'A05p30930' => 'bna', 'A07p15190' => 'bna', 'Aa31LG8G5190' => 'aar', 'Aa31LG8G5520' => 'aar', 'Actinidia15150' => 'ach', 'Ah.05g167620' => 'amhyb', 'Ah.08g220510' => 'amhyb', 'AL1G34420' => 'aly', 'AL2G27310' => 'aly', 'AL3G31640' => 'aly', 'AL3G32010' => 'aly', 'AL3G32030' => 'aly', 'Aqoxy1G00584' => 'aox', 'Aqoxy3G00278' => 'aox', 'Aqoxy5G03540' => 'aox', 'Aqoxy6G00387' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407XUT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6A166J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZ5XB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XR04TG' => 'arhy', 'AT1G21326' => 'ath', 'AT1G68450' => 'ath', 'AT3G18360' => 'ath', 'AT3G18690' => 'ath', 'ATR0697G169' => 'atr', 'ATR0772G190' => 'atr', 'ATR1125G102' => 'atr', 'Atru.chr11.114' => 'acertr', 'Atru.chr13.2242' => 'acertr', 'Atru.chr4.785' => 'acertr', 'Atru.chr8.1283' => 'acertr', 'Atru.chr8.665' => 'acertr', 'AUR62003608' => 'cqu', 'AUR62013512' => 'cqu', 'AUR62017919' => 'cqu', 'AUR62026761' => 'cqu', 'AUR62035203' => 'cqu', 'BcaB03g14273' => 'bca', 'BcaB04g18998' => 'bca', 'BcaB04g20756' => 'bca', 'BcaB05g24382' => 'bca', 'BcaB06g25879' => 'bca', 'BcaB06g25920' => 'bca', 'BcaB07g32119' => 'bca', 'BcaC01g03684' => 'bca', 'BcaC03g14948' => 'bca', 'BcaC05g26036' => 'bca', 'BcaC05g28582' => 'bca', 'BcaC06g34871' => 'bca', 'BcaC09g48794' => 'bca', 'BcaC09g48824' => 'bca', 'BcaNung04873' => 'bca', 'BolC1t04518H' => 'bol', 'BolC1t04547H' => 'bol', 'BolC2t08559H' => 'bol', 'BolC3t17262H' => 'bol', 'BolC5t33415H' => 'bol', 'BraA01t03658Z' => 'bra', 'BraA01t03679Z' => 'bra', 'BraA02t06567Z' => 'bra', 'BraA03t13235Z' => 'bra', 'BraA05t21935Z' => 'bra', 'C01p45550' => 'bna', 'C01p45850' => 'bna', 'C02p24610' => 'bna', 'C03p49650' => 'bna', 'C05p46850' => 'bna', 'C07p22310' => 'bna', 'CAN.G1425.4' => 'can', 'CAN.G1425.6' => 'can', 'CAN.G1664.1' => 'can', 'CAN.G62.47' => 'can', 'CANSAT01G1945' => 'cansat', 'CANSAT01G2763' => 'cansat', 'CANSAT25G0717' => 'cansat', 'CANSAT64G0006' => 'cansat', 'CARHR021710' => 'chi', 'CARHR061230' => 'chi', 'CARHR093710' => 'chi', 'CARHR094070' => 'chi', 'Carub.0001s2072' => 'cru', 'Carub.0002s1496' => 'cru', 'Carub.0003s1814' => 'cru', 'Carub.0003s1847' => 'cru', 'Ca_11163_v3' => 'car', 'Ca_16665_v3' => 'car', 'Ca_16927_v3' => 'car', 'Ca_25487_v3' => 'car', 'Ca_28450_v3' => 'car', 'Cc03_g13430' => 'ccan', 'Cc07_g17900' => 'ccan', 'Cc10_g14190' => 'ccan', 'Cc11_g10020' => 'ccan', 'CDE04G0760' => 'cde', 'CDE04G3497' => 'cde', 'CDE06G0770' => 'cde', 'CDE06G1589' => 'cde', 'CDE08G0005' => 'cde', 'Cfa002833' => 'cfa', 'Cfa018343' => 'cfa', 'Cfa019761' => 'cfa', 'Cfa020066' => 'cfa', 'Cfa020067' => 'cfa', 'Ciclev10002106m.g' => 'ccl', 'Ciclev10013749m.g' => 'ccl', 'Ciclev10023693m.g' => 'ccl', 'Ciclev10023791m.g' => 'ccl', 'Ciclev10026434m.g' => 'ccl', 'CiPaw.03G128100' => 'cil', 'CiPaw.04G086200' => 'cil', 'CiPaw.09G024300' => 'cil', 'CiPaw.10G021400' => 'cil', 'CiPaw.15G019500' => 'cil', 'CiPaw.15G086400' => 'cil', 'CiPaw.15G086500' => 'cil', 'CiPaw.15G131400' => 'cil', 'CiPaw.16G016300' => 'cil', 'CiPaw.16G065400' => 'cil', 'ClCG02G000620' => 'cla', 'ClCG05G022640' => 'cla', 'ClCG06G014760' => 'cla', 'ClCG08G006550' => 'cla', 'ClCG10G017960' => 'cla', 'COL.COLO4_03433' => 'col', 'COL.COLO4_07638' => 'col', 'COL.COLO4_14006' => 'col', 'COL.COLO4_21539' => 'col', 'COL.COLO4_29493' => 'col', 'COL.COLO4_32831' => 'col', 'COL.COLO4_36019' => 'col', 'Cpa.g.c35103' => 'cpa', 'Cpa.g.c39771' => 'cpa', 'Cpa.g.sc1.29' => 'cpa', 'Cpa.g.sc3.505' => 'cpa', 'Cpa.g.sc42.113' => 'cpa', 'Cpa.g.sc49.45' => 'cpa', 'Cpa.g.sc49.47' => 'cpa', 'CsaV3_2G018150' => 'csa', 'CsaV3_2G025160' => 'csa', 'CsaV3_3G038330' => 'csa', 'CsaV3_5G034400' => 'csa', 'CsaV3_6G030890' => 'csa', 'CSS0012233' => 'camsi', 'CSS0020698' => 'camsi', 'CSS0032299' => 'camsi', 'CSS0034671' => 'camsi', 'CSS0038492' => 'camsi', 'CSS0040830' => 'camsi', 'DCAR_001091' => 'dca', 'DCAR_001357' => 'dca', 'DCAR_014345' => 'dca', 'DCAR_014416' => 'dca', 'DCAR_014417' => 'dca', 'DCAR_023208' => 'dca', 'DCAR_026737' => 'dca', 'Dinv11325' => 'din', 'Dinv21073' => 'din', 'Dinv24322' => 'din', 'Dinv25835' => 'din', 'Dinv28111' => 'din', 'Dinv31630' => 'din', 'Duzib041G0538' => 'dzi', 'Duzib084G0272' => 'dzi', 'Duzib093G1110' => 'dzi', 'Duzib093G1352' => 'dzi', 'Duzib116G0881' => 'dzi', 'Duzib128G1674' => 'dzi', 'Duzib147G0658' => 'dzi', 'Duzib187G0304' => 'dzi', 'Duzib205G0230' => 'dzi', 'Duzib264G1003' => 'dzi', 'Duzib268G0437' => 'dzi', 'ECA194G0008' => 'eca', 'ECA233G1288' => 'eca', 'ECA233G1982' => 'eca', 'ECA236G4231' => 'eca', 'ECA238G3992' => 'eca', 'ECA238G4256' => 'eca', 'ECA246G2987' => 'eca', 'ECA247G3141' => 'eca', 'EL10Ac1g01490' => 'bvu', 'EL10Ac5g11455' => 'bvu', 'EL10Ac6g14383' => 'bvu', 'EL10Ac6g15268' => 'bvu', 'Eucgr.A02544' => 'egr', 'Eucgr.C02621' => 'egr', 'Eucgr.C02629' => 'egr', 'Eucgr.F02723' => 'egr', 'Eucgr.G02312' => 'egr', 'Eucgr.I00226' => 'egr', 'FAN02G0442' => 'fan', 'FAN04G0269' => 'fan', 'FAN05G1048' => 'fan', 'FAN05G4110' => 'fan', 'FAN07G0491' => 'fan', 'FAN08G3585' => 'fan', 'FAN12G0246' => 'fan', 'FAN12G0708' => 'fan', 'FAN13G2378' => 'fan', 'FAN14G0712' => 'fan', 'FAN15G3153' => 'fan', 'FAN17G0570' => 'fan', 'FAN18G1152' => 'fan', 'FAN18G4498' => 'fan', 'FAN19G1131' => 'fan', 'FAN20G2326' => 'fan', 'FAN22G0160' => 'fan', 'FAN23G1856' => 'fan', 'FAN24G3322' => 'fan', 'FAN26G1531' => 'fan', 'FAN27G1120' => 'fan', 'FAN28G0084' => 'fan', 'FvH4_1g24040' => 'fve', 'FvH4_2g14340' => 'fve', 'FvH4_4g27220' => 'fve', 'FvH4_5g11980' => 'fve', 'FvH4_6g21030' => 'fve', 'Glyma.03G204900' => 'gma', 'Glyma.04G214700' => 'gma', 'Glyma.04G239400' => 'gma', 'Glyma.05G190000' => 'gma', 'Glyma.06G124400' => 'gma', 'Glyma.06G151400' => 'gma', 'Glyma.07G092500' => 'gma', 'Glyma.08G041900' => 'gma', 'Glyma.08G147600' => 'gma', 'Glyma.09G183700' => 'gma', 'Glyma.10G273300' => 'gma', 'Glyma.13G039800' => 'gma', 'Glyma.14G124800' => 'gma', 'Glyma.19G202300' => 'gma', 'Glyma.20G116600' => 'gma', 'Gohir.A01G199550' => 'ghi', 'Gohir.A02G108503' => 'ghi', 'Gohir.A05G321500' => 'ghi', 'Gohir.A08G093800' => 'ghi', 'Gohir.A10G083607' => 'ghi', 'Gohir.A12G001200' => 'ghi', 'Gohir.D01G123101' => 'ghi', 'Gohir.D01G189650' => 'ghi', 'Gohir.D03G070700' => 'ghi', 'Gohir.D05G323700' => 'ghi', 'Gohir.D07G211466' => 'ghi', 'Gohir.D08G105100' => 'ghi', 'Gohir.D10G106100' => 'ghi', 'Gohir.D12G000900' => 'ghi', 'Gorai.002G154000' => 'gra', 'Gorai.002G233400' => 'gra', 'Gorai.003G089500' => 'gra', 'Gorai.004G112000' => 'gra', 'Gorai.008G000200' => 'gra', 'Gorai.009G347500' => 'gra', 'Gorai.011G116000' => 'gra', 'GSVIVG01001661001' => 'vvi', 'HanXRQChr02g0037451' => 'han', 'HanXRQChr04g0109411' => 'han', 'HanXRQChr12g0364621' => 'han', 'HanXRQChr12g0364631' => 'han', 'Haze_17495' => 'cav', 'Haze_17728' => 'cav', 'Haze_18687' => 'cav', 'Haze_20128' => 'cav', 'Haze_20129' => 'cav', 'Haze_25129' => 'cav', 'Hma1.2p1_0006F.1_g004610' => 'hma', 'Hma1.2p1_0061F.1_g033760' => 'hma', 'Hma1.2p1_0483F.1_g162740' => 'hma', 'Hma1.2p1_0653F.1_g196240' => 'hma', 'HPP92_000062' => 'vpl', 'HPP92_000981' => 'vpl', 'HPP92_001096' => 'vpl', 'HPP92_003212' => 'vpl', 'HPP92_004812' => 'vpl', 'HPP92_004813' => 'vpl', 'HPP92_004816' => 'vpl', 'HPP92_011921' => 'vpl', 'HPP92_011922' => 'vpl', 'HPP92_011923' => 'vpl', 'HPP92_016162' => 'vpl', 'HPP92_026215' => 'vpl', 'HPP92_027454' => 'vpl', 'Lalb_Chr04g0254691' => 'lal', 'Lalb_Chr05g0222471' => 'lal', 'Lalb_Chr06g0166031' => 'lal', 'Lalb_Chr07g0184491' => 'lal', 'Lalb_Chr11g0066501' => 'lal', 'Lalb_Chr13g0296541' => 'lal', 'Lalb_Chr16g0387891' => 'lal', 'Lalb_Chr21g0308871' => 'lal', 'Lalb_Chr22g0353121' => 'lal', 'Lalb_Chr23g0271401' => 'lal', 'Lj1g0004766' => 'lja', 'Lj2g0004597' => 'lja', 'Lj2g0018313' => 'lja', 'Lj4g0014153' => 'lja', 'Lj4g0024168' => 'lja', 'Lj4P850T14' => 'lonja', 'Lj5C278T5' => 'lonja', 'Lj5g0015241' => 'lja', 'Lj7P367T19' => 'lonja', 'Lsat_1_v5_gn_1_8801' => 'lsa', 'Lsat_1_v5_gn_2_14741' => 'lsa', 'Lsat_1_v5_gn_6_34220' => 'lsa', 'Lsat_1_v5_gn_8_40921' => 'lsa', 'Lsat_1_v5_gn_9_40280' => 'lsa', 'Manes.01G010900' => 'mes', 'Manes.02G176600' => 'mes', 'Manes.06G067000' => 'mes', 'Manes.08G037400' => 'mes', 'Manes.12G152600' => 'mes', 'Manes.14G103400' => 'mes', 'Manes.18G089366' => 'mes', 'Mapoly0010s0102' => 'mpo', 'MBI09_g40766_MAGBIO' => 'mbi', 'MBI16_g32670_MAGBIO' => 'mbi', 'MBI17_g11165_MAGBIO' => 'mbi', 'MD01G1011800' => 'mdo', 'MD05G1018300' => 'mdo', 'MD10G1018000' => 'mdo', 'MD15G1338100' => 'mdo', 'MD16G1041600' => 'mdo', 'Medtr1g028910' => 'mtr', 'Medtr1g028920' => 'mtr', 'Medtr1g110570' => 'mtr', 'Medtr3g090350' => 'mtr', 'Medtr3g095820' => 'mtr', 'Medtr6g084200' => 'mtr', 'Medtr8g093335' => 'mtr', 'Medtr8g093390' => 'mtr', 'MELO3C008398.2' => 'cme', 'MELO3C009575.2' => 'cme', 'MELO3C010713.2' => 'cme', 'MELO3C017312.2' => 'cme', 'MELO3C023257.2' => 'cme', 'MELO3C027191.2' => 'cme', 'Migut.C01025' => 'egut', 'Migut.H00745' => 'egut', 'Migut.J00487' => 'egut', 'Migut.L01057' => 'egut', 'MSTRG.2669' => 'ama', 'MSTRG.847' => 'ama', 'Nitab4.5_0000299g0270' => 'nta', 'Nitab4.5_0000427g0090' => 'nta', 'Nitab4.5_0000489g0090' => 'nta', 'Nitab4.5_0000633g0120' => 'nta', 'Nitab4.5_0001674g0050' => 'nta', 'Nitab4.5_0002121g0030' => 'nta', 'Nitab4.5_0002906g0010' => 'nta', 'Nitab4.5_0004813g0010' => 'nta', 'Nitab4.5_0006679g0010' => 'nta', 'Nn1g06171' => 'nnu', 'Nn2g14422' => 'nnu', 'Nn3g17865' => 'nnu', 'Nn4g23866' => 'nnu', 'Nn5g28668' => 'nnu', 'Oeu001004.1' => 'oeu', 'Oeu002640.2' => 'oeu', 'Oeu008243.1' => 'oeu', 'Oeu014479.1' => 'oeu', 'Oeu024887.1' => 'oeu', 'Oeu032976.1' => 'oeu', 'Oeu034232.1' => 'oeu', 'Oeu037616.1' => 'oeu', 'Oeu046011.1' => 'oeu', 'Oeu046984.1' => 'oeu', 'Oeu051260.1' => 'oeu', 'Os02g0539500' => 'osa', 'Os03g0267400' => 'osa', 'Os04g0417600' => 'osa', 'Os08g0102900' => 'osa', 'Os10g0575401' => 'osa', 'Peaxi162Scf00012g00206' => 'pax', 'Peaxi162Scf00013g01028' => 'pax', 'Peaxi162Scf00015g00106' => 'pax', 'Peaxi162Scf00051g00055' => 'pax', 'Peaxi162Scf00263g00083' => 'pax', 'PGR042G2791' => 'pgr', 'PGR044G0866' => 'pgr', 'PGR102G1908' => 'pgr', 'PGR119G0869' => 'pgr', 'PGR119G2222' => 'pgr', 'PGR142G3041' => 'pgr', 'PGSC0003DMG400000771' => 'stu', 'PGSC0003DMG400005637' => 'stu', 'PGSC0003DMG400017564' => 'stu', 'PGSC0003DMG400028672' => 'stu', 'PGSC0003DMG401028780' => 'stu', 'Phvul.002G270600' => 'pvu', 'Phvul.003G030601' => 'pvu', 'Phvul.004G156300' => 'pvu', 'Phvul.007G028200' => 'pvu', 'Phvul.008G159700' => 'pvu', 'Phvul.009G136500' => 'pvu', 'Phvul.009G148500' => 'pvu', 'Potri.002G070600' => 'ptr', 'Potri.005G057800' => 'ptr', 'Potri.005G189300' => 'ptr', 'Potri.006G199300' => 'ptr', 'Potri.007G110100' => 'ptr', 'Potri.008G121650' => 'ptr', 'Potri.010G123700' => 'ptr', 'Potri.012G055900' => 'ptr', 'Potri.015G046600' => 'ptr', 'Pp3c10_7810' => 'ppa', 'Pp3c16_22640' => 'ppa', 'Pp3c25_12310' => 'ppa', 'Pp3c25_12370' => 'ppa', 'Pp3c5_24370' => 'ppa', 'Pp3c5_24450' => 'ppa', 'Pp3c6_4170' => 'ppa', 'Prupe.1G312500' => 'ppe', 'Prupe.2G000100' => 'ppe', 'Prupe.5G222000' => 'ppe', 'Prupe.8G022500' => 'ppe', 'Psat1g034720' => 'psa', 'Psat5g061000' => 'psa', 'Psat5g061680' => 'psa', 'Psat5g080400' => 'psa', 'Psat6g226600' => 'psa', 'Psat6g227240' => 'psa', 'Psat7g047880' => 'psa', 'PSO210G1654' => 'pso', 'PSO541G5231' => 'pso', 'PSO541G6297' => 'pso', 'PSO675G0766' => 'pso', 'PSO675G7373' => 'pso', 'QL01p041163' => 'qlo', 'QL01p041179' => 'qlo', 'QL02p024757' => 'qlo', 'QL06p029571' => 'qlo', 'QL06p036159' => 'qlo', 'QL07p026339' => 'qlo', 'QL10p025510' => 'qlo', 'RcHm_v2.0_Chr2g0120181' => 'rch', 'RcHm_v2.0_Chr4g0435011' => 'rch', 'RcHm_v2.0_Chr6g0276681' => 'rch', 'Rhsim03G0008700' => 'rsi', 'Rhsim08G0003200' => 'rsi', 'Rhsim08G0133100' => 'rsi', 'Rhsim09G0107000' => 'rsi', 'Sabra02G0055300' => 'sbr', 'Sabra05G0049800' => 'sbr', 'Sabra05G0144600' => 'sbr', 'Sabra06G0153200' => 'sbr', 'Sabra07G0090100' => 'sbr', 'Sabra10G0093700' => 'sbr', 'Sabra12G0039700' => 'sbr', 'Sabra15G0039100' => 'sbr', 'SalBow7G3795' => 'sbo', 'SalBow8G5321' => 'sbo', 'Sc07g0001670' => 'sci', 'Sc20g0003400' => 'sci', 'Sed0003786' => 'sed', 'Sed0007872' => 'sed', 'Sed0010828' => 'sed', 'Sed0011999' => 'sed', 'Sed0014716' => 'sed', 'Sed0016046' => 'sed', 'Sed0025511' => 'sed', 'Sed0028138' => 'sed', 'SEGI_38755' => 'sgi', 'SEGI_39381' => 'sgi', 'SGA_v2.0_scaffold250G45000' => 'sas', 'SGA_v2.0_scaffold38G14938' => 'sas', 'SGA_v2.0_scaffold48G17954' => 'sas', 'SMO119G0292' => 'smo', 'Solyc03g119410.1' => 'sly', 'Solyc06g060470.1' => 'sly', 'Solyc11g005720.1' => 'sly', 'Sopen04g026910' => 'spe', 'Sopen06g020590' => 'spe', 'Sopen11g001680' => 'spe', 'Sp1g18880' => 'spa', 'Sp3g16470' => 'spa', 'Sp3g16760' => 'spa', 'Sp5g23520' => 'spa', 'TAR369G0643' => 'tar', 'TAR371G0320' => 'tar', 'TAR376G0474' => 'tar', 'TAR381G0526' => 'tar', 'TAR579G0002' => 'tar', 'TAR623G0067' => 'tar', 'TAR628G0442' => 'tar', 'TAR629G0393' => 'tar', 'TAR629G3519' => 'tar', 'THA.LOC104806066' => 'tha', 'THA.LOC104812050' => 'tha', 'THA.LOC104820391' => 'tha', 'THA.LOC104821856' => 'tha', 'THA.LOC104821926' => 'tha', 'THA.LOC109117016' => 'tha', 'Thecc.01G125600' => 'tca', 'Thecc.02G227800' => 'tca', 'Thecc.03G036500' => 'tca', 'Thecc.05G110300' => 'tca', 'Thecc.08G146900' => 'tca', 'Thhalv10008673m.g' => 'esa', 'Thhalv10019299m.g' => 'esa', 'Thhalv10021464m.g' => 'esa', 'Thhalv10022101m.g' => 'esa', 'TPR.G15166' => 'tpr', 'TPR.G18777' => 'tpr', 'TPR.G18807' => 'tpr', 'TPR.G29601' => 'tpr', 'TWI31G0680' => 'twi', 'TWI32G1022' => 'twi', 'TWI34G0256' => 'twi', 'TWI60G0870' => 'twi', 'TWI79G1231' => 'twi', 'TWI79G1623' => 'twi', 'TWI81G0318' => 'twi', 'unitig_22.g6558' => 'ugi', 'unitig_82.g27038' => 'ugi', 'unitig_899.g14702' => 'ugi', 'VMungo0251G0634' => 'vmu', 'VMungo0464G1252' => 'vmu', 'VMungo1215G0327' => 'vmu', 'VMungo1309G1275' => 'vmu', 'VMungo1309G2779' => 'vmu', 'Zm00001eb083470' => 'zma', 'Zm00001eb259970' => 'zma', 'Zm00001eb434260' => 'zma' ) $gf_id = 'HOM05D001186' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001186' ) $data_identifier = 'HOM05D001186' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'ach' => (int) 1, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 15, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 10, 'cla' => (int) 5, 'col' => (int) 7, 'cpa' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 22, 'fve' => (int) 5, 'gma' => (int) 15, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 1, 'han' => (int) 4, 'cav' => (int) 6, 'hma' => (int) 4, 'vpl' => (int) 13, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 2, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 9, 'ppa' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 8, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 8, 'sgi' => (int) 2, 'sas' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb434260' $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